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First I did a complete scan on C:\ and kept getting (after about 1.5M files scanned, which is at the end of the C:\ProgramData folder or the beginning of the C:\Recovery folder)

enter image description here

Then, after scanning the C:\ProgramData folder for approximately 38000-39000 files, SE will got stuck in the following way:

  • It will make no progress in 'Time elapsed', 'Items scanned', and 'item'.
  • it cannot be stopped from the 'Cancel Scan' button; cancelling the task in Task Manager is the only way I can do it (it will still display a status of 'Running' in the Task Manager).

In the latest three runs, it has been after the 38082th file in C:\ProgramData, but before that it has stopped at 39030. Further, when it used to stop in a particular file in the Skype subfolder (Skype.msi->sv-se.mst), I deleted the entire subfolder without any improvement, so it probably isn't the particular file it displays last that is causing the halt.

After selecting smaller and smaller subsets within the ProgramData folder, to see where it breaks, I pinned down the C:\ProgramData\Microsoft folder. However, now when I scan anything, it will not do anything (even after restarting SE): enter image description here

Either I have restarted SE (followed by a scan it didn't like) too many times and something got broken or I have malware. I don;t want to reboot because it is obviously bad in the latter scenario.

I'm using Windows 7 64bit. Security Essentials has the latest definitions. Emisoft Malaware didn't find anything.

Not sure if the following is relevant but I also noticed that this executable has been crashing lately in the log:

enter image description here

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Have you tried a Chkdsk? How about reinstalling MSE? –  Ƭᴇcʜιᴇ007 Apr 13 '13 at 15:15
    
Thanks for the tip. I have an SSD, should I check both "Automatically fix file system errors" and "scan for and attempt recovery of bad sectors"? I have had about two dozen BSOD's in the last year, so it could easily be corruption. –  Wuschelbeutel Kartoffelhuhn Apr 14 '13 at 1:51

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